4HV4 | pdb_00004hv4

2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb4HV4/pdb

• Classification: LIGASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-11-05 Released: 2012-11-21 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP

Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.84 kDa 
• Atom Count: 7,602 
• Modeled Residue Count: 927 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate--L-alanine ligase	A, B	494	Yersinia pestis CO92	Mutation(s): 0  Gene Names: murC, y3625, YPO0556, YP_3628 EC: 6.3.2.8
UniProt
Find proteins for Q8ZIE8 (Yersinia pestis) Explore Q8ZIE8  Go to UniProtKB:  Q8ZIE8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
BME	D [auth A], F [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34hv4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.534	α = 90
b = 78.021	β = 90
c = 183.296	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description